Cell Initial Conditions

createICCellXMLTemplate(folder::String)

Create folder with a template XML file for IC cells.

See the PhysiCellCellCreator.jl documentation for more information on IC cells and how this function works outside of pcvct. This pcvct function runs the createICCellXMLTemplate function from PhysiCellCellCreator.jl and then updates the database. Furthermore, the folder can be passed in just as the name of the folder located in data/inputs/ics/cells/ rather than the full path.

This functionality is run outside of a PhysiCell runtime. It will not work in PhysiCell! This function creates a template XML file for IC cells, showing all the current functionality of this initialization scheme. It uses the cell type "default". Create ICs for more cell types by copying the cell_patches element. The ID attribute in patch elements is there exactly to allow variations to target specific patches. Manually maintain these or you will not be able to vary specific patches effectively.

Each time a simulation is run that is using a cells.xml file, a new CSV file will be created, drawing randomly from the patches defined in the XML file. These will all be stored with data/inputs/ics/cells/folder/ic_cell_variations as ic_cell_variation_#_s#.csv where the first # is the variation ID associated with variation on the XML file and the second # is the simulation ID. Importantly, no two simulations will use the same CSV file.